Results 41 to 50 of about 669,188 (305)
RuleMonkey: software for stochastic simulation of rule-based models
BMC Bioinformatics, 2010 Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen ...
Hlavacek William S +5 more
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Delays in Model Reduction of Chemical Reaction Networks
IFAC-PapersOnLine, 2018 Abstract A novel engineering model reduction method is proposed in this paper that can be applied to a chemical reaction network (CRN) with chains of linear reactions. The reduced model is a delayed CRN with possibly different delays but with less state variables than the original model.
György Lipták, Katalin M. Hangos
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Efficient multi-fidelity computation of blood coagulation under flow.
PLoS Computational Biology, 2023 Clot formation is a crucial process that prevents bleeding, but can lead to severe disorders when imbalanced. This process is regulated by the coagulation cascade, a biochemical network that controls the enzyme thrombin, which converts soluble fibrinogen
Manuel Guerrero-Hurtado +8 more
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Predicting potentially hazardous chemical reactions using an explainable neural network
Chemical Science, 2021 Predicting potentially dangerous chemical reactions is a critical task for laboratory safety. However, a traditional experimental investigation of reaction conditions for possible hazardous or explosive byproducts entails substantial time and cost, for ...
Juhwan Kim +6 more
semanticscholar +1 more source
Generic Strategies for Chemical Space Exploration [PDF]
, 2014 Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial explosion.
Andersen, Jakob L. +3 more
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A reaction network approach to the convergence to equilibrium of quantum Boltzmann equations for Bose gases [PDF]
E S A I M: Control, Optimisation and Calculus of Variations, 2016 When the temperature of a trapped Bose gas is below the Bose-Einstein transition temperature and above absolute zero, the gas is composed of two distinct components: the Bose-Einstein condensate and the cloud of thermal excitations.
G. Craciun, Minh-Binh Tran
semanticscholar +1 more source
Piecewise linear models of chemical reaction networks
, 2012 We show that certain non-linear dynamical systems with non-linearities in the form of Hill functions, can be approximated by piecewise linear dynamical systems. The resulting piecewise systems have closed form solutions that can be used to understand the behavior of the fully nonlinear system.
Kumar, Ajit, Josić, Krešimir
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A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. [PDF]
PLoS Computational Biology, 2012 The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology.
Daniele De Martino +3 more
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Exploiting network topology for large-scale inference of nonlinear reaction models
, 2019 The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to estimate unknown
Galagali, Nikhil, Marzouk, Youssef M.
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Reduction of dynamical biochemical reaction networks in computational biology [PDF]
, 2012 Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression.
Gorban, Alexander N. +3 more
core +6 more sources